aics-imageio fails to open .tif files #77
Comments
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I think this might be the same as: |
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@psobolewskiPhD thanks a lot for the tipp. Activating "Use npe2 adaptor" in Preferences->Plugins as suggested by @DragaDoncila fixed the issue for me. However, activating the npe2 adaptor broke the tools menu. Hence I decided to downgrade npe2 to v0.6.2 after all. Maybe this could find its way into the readme under installation? |
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I think this will all be fixed with the 0.4.18 release, which is ComingSoonTM (no seriously, we're working on it!) |
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sounds great, looking forward 😄 |
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Hi,
thank you so much for providing this great reader plugin for napari. It has helped me a lot!
However, in the recent version, when I try to open .tif files, I get the following error message in napari:
full error traceback
--------------------------------------------------------------------------- ValueError Traceback (most recent call last) File ~\mambaforge\envs\vanilla-napari\lib\site-packages\napari\_qt\qt_viewer.py:748, in QtViewer._open_files_dialog(self=, choose_plugin=False) 747 for filename in filenames: --> 748 self._qt_open( self = filename = 'Z:/Till/188_viventis_data/downscaled_mCherry-1.tif' [filename] = ['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'] choose_plugin = False 749 [filename], stack=False, choose_plugin=choose_plugin 750 ) 751 update_open_history(filenames[0])File ~\mambaforge\envs\vanilla-napari\lib\site-packages\napari_qt\qt_viewer.py:848, in QtViewer._qt_open(self=<napari._qt.qt_viewer.QtViewer object>, filenames=['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'], stack=False, choose_plugin=False, plugin=None, layer_type=None, **kwargs={})
847 except MultipleReaderError:
--> 848 handle_gui_reading(filenames, self, stack, **kwargs)
filenames = ['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif']
self = <napari._qt.qt_viewer.QtViewer object at 0x000001CA466F3490>
stack = False
kwargs = {}
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\napari_qt\dialogs\qt_reader_dialog.py:199, in handle_gui_reading(paths=['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'], qt_viewer=<napari._qt.qt_viewer.QtViewer object>, stack=False, plugin_name=None, error=None, plugin_override=False, **kwargs={})
198 if display_name:
--> 199 open_with_dialog_choices(
display_name = 'aicsimageio-in-memory'
persist = False
readerDialog = <napari._qt.dialogs.qt_reader_dialog.QtReaderDialog object at 0x000001CA55805900>
readerDialog._extension = '.tif'
readers = {'aicsimageio-in-memory': 'aicsimageio-in-memory', 'aicsimageio-out-of-memory': 'aicsimageio-out-of-memory', 'napari': 'napari builtins'}
paths = ['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif']
stack = False
qt_viewer = <napari._qt.qt_viewer.QtViewer object at 0x000001CA466F3490>
kwargs = {}
200 display_name,
201 persist,
202 readerDialog._extension,
203 readers,
204 paths,
205 stack,
206 qt_viewer,
207 **kwargs,
208 )
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\napari_qt\dialogs\qt_reader_dialog.py:292, in open_with_dialog_choices(display_name='aicsimageio-in-memory', persist=False, extension='.tif', readers={'aicsimageio-in-memory': 'aicsimageio-in-memory', 'aicsimageio-out-of-memory': 'aicsimageio-out-of-memory', 'napari': 'napari builtins'}, paths=['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'], stack=False, qt_viewer=<napari._qt.qt_viewer.QtViewer object>, **kwargs={})
291 # may throw error, but we let it this time
--> 292 qt_viewer.viewer.open(paths, stack=stack, plugin=plugin_name, **kwargs)
plugin_name = 'aicsimageio-in-memory'
paths = ['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif']
qt_viewer.viewer = Viewer(axes=Axes(visible=False, labels=True, colored=True, dashed=False, arrows=True), camera=Camera(center=(0.0, 0.0, 0.0), zoom=1.0, angles=(0.0, 0.0, 90.0), perspective=0.0, interactive=True), cursor=Cursor(position=(1.0, 1.0), scaled=True, size=1, style=<CursorStyle.STANDARD: 'standard'>), dims=Dims(ndim=2, ndisplay=2, last_used=0, range=((0, 2, 1), (0, 2, 1)), current_step=(0, 0), order=(0, 1), axis_labels=('0', '1')), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layers=[], scale_bar=ScaleBar(visible=False, colored=False, color=<class 'numpy.ndarray'> (4,) float32, ticks=True, position=<Position.BOTTOM_RIGHT: 'bottom_right'>, font_size=10.0, box=False, box_color=<class 'numpy.ndarray'> (4,) float32, unit=None), text_overlay=TextOverlay(visible=False, color=<class 'numpy.ndarray'> (4,) float32, font_size=10.0, position=<TextOverlayPosition.TOP_LEFT: 'top_left'>, text=''), overlays=Overlays(interaction_box=InteractionBox(points=None, show=False, show_handle=False, show_vertices=False, selection_box_drag=None, selection_box_final=None, transform_start=<napari.utils.transforms.transforms.Affine object at 0x000001CA3FAA4EE0>, transform_drag=<napari.utils.transforms.transforms.Affine object at 0x000001CA3FAA4F40>, transform_final=<napari.utils.transforms.transforms.Affine object at 0x000001CA3FAA4FA0>, transform=<napari.utils.transforms.transforms.Affine object at 0x000001CA3FAA5000>, allow_new_selection=True, selected_vertex=None)), help='', status='Ready', tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_over_canvas=True, mouse_move_callbacks=[<function InteractionBoxMouseBindings.initialize_mouse_events..mouse_move at 0x000001CA51722680>], mouse_drag_callbacks=[<function InteractionBoxMouseBindings.initialize_mouse_events..mouse_drag at 0x000001CA51722950>], mouse_double_click_callbacks=[], mouse_wheel_callbacks=[<function dims_scroll at 0x000001CA4560EEF0>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keymap={'Shift': <function InteractionBoxMouseBindings.initialize_key_events..hold_to_lock_aspect_ratio at 0x000001CA517227A0>, 'Control-Shift-R': <function InteractionBoxMouseBindings._reset_active_layer_affine at 0x000001CA520F40D0>, 'Control-Shift-A': <function InteractionBoxMouseBindings._transform_active_layer at 0x000001CA520F4C10>})
stack = False
kwargs = {}
qt_viewer = <napari._qt.qt_viewer.QtViewer object at 0x000001CA466F3490>
294 if persist:
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\napari\components\viewer_model.py:1014, in ViewerModel.open(self=Viewer(axes=Axes(visible=False, labels=True, col...._transform_active_layer at 0x000001CA520F4C10>}), path=['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'], stack=False, plugin='aicsimageio-in-memory', layer_type=None, **kwargs={})
1012 if plugin:
1013 added.extend(
-> 1014 self._add_layers_with_plugins(
added = []
self = Viewer(axes=Axes(visible=False, labels=True, colored=True, dashed=False, arrows=True), camera=Camera(center=(0.0, 0.0, 0.0), zoom=1.0, angles=(0.0, 0.0, 90.0), perspective=0.0, interactive=True), cursor=Cursor(position=(1.0, 1.0), scaled=True, size=1, style=<CursorStyle.STANDARD: 'standard'>), dims=Dims(ndim=2, ndisplay=2, last_used=0, range=((0, 2, 1), (0, 2, 1)), current_step=(0, 0), order=(0, 1), axis_labels=('0', '1')), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layers=[], scale_bar=ScaleBar(visible=False, colored=False, color=<class 'numpy.ndarray'> (4,) float32, ticks=True, position=<Position.BOTTOM_RIGHT: 'bottom_right'>, font_size=10.0, box=False, box_color=<class 'numpy.ndarray'> (4,) float32, unit=None), text_overlay=TextOverlay(visible=False, color=<class 'numpy.ndarray'> (4,) float32, font_size=10.0, position=<TextOverlayPosition.TOP_LEFT: 'top_left'>, text=''), overlays=Overlays(interaction_box=InteractionBox(points=None, show=False, show_handle=False, show_vertices=False, selection_box_drag=None, selection_box_final=None, transform_start=<napari.utils.transforms.transforms.Affine object at 0x000001CA3FAA4EE0>, transform_drag=<napari.utils.transforms.transforms.Affine object at 0x000001CA3FAA4F40>, transform_final=<napari.utils.transforms.transforms.Affine object at 0x000001CA3FAA4FA0>, transform=<napari.utils.transforms.transforms.Affine object at 0x000001CA3FAA5000>, allow_new_selection=True, selected_vertex=None)), help='', status='Ready', tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_over_canvas=True, mouse_move_callbacks=[<function InteractionBoxMouseBindings.initialize_mouse_events..mouse_move at 0x000001CA51722680>], mouse_drag_callbacks=[<function InteractionBoxMouseBindings.initialize_mouse_events..mouse_drag at 0x000001CA51722950>], mouse_double_click_callbacks=[], mouse_wheel_callbacks=[<function dims_scroll at 0x000001CA4560EEF0>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keymap={'Shift': <function InteractionBoxMouseBindings.initialize_key_events..hold_to_lock_aspect_ratio at 0x000001CA517227A0>, 'Control-Shift-R': <function InteractionBoxMouseBindings._reset_active_layer_affine at 0x000001CA520F40D0>, 'Control-Shift-A': <function InteractionBoxMouseBindings._transform_active_layer at 0x000001CA520F4C10>})
_path = ['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif']
kwargs = {}
plugin = 'aicsimageio-in-memory'
layer_type = None
_stack = False
1015 _path,
1016 kwargs=kwargs,
1017 plugin=plugin,
1018 layer_type=layer_type,
1019 stack=_stack,
1020 )
1021 )
1022 # no plugin choice was made
1023 else:
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\napari\components\viewer_model.py:1216, in ViewerModel._add_layers_with_plugins(self=Viewer(axes=Axes(visible=False, labels=True, col...._transform_active_layer at 0x000001CA520F4C10>}), paths=['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'], stack=False, kwargs={}, plugin='aicsimageio-in-memory', layer_type=None)
1215 assert len(paths) == 1
-> 1216 layer_data, hookimpl = read_data_with_plugins(
paths = ['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif']
stack = False
plugin = 'aicsimageio-in-memory'
1217 paths, plugin=plugin, stack=stack
1218 )
1220 # glean layer names from filename. These will be used as fallback
1221 # names, if the plugin does not return a name kwarg in their meta dict.
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\napari\plugins\io.py:77, in read_data_with_plugins(paths=['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'], plugin='aicsimageio-in-memory', stack=False)
75 hookimpl: Optional[HookImplementation]
---> 77 res = _npe2.read(paths, plugin, stack=stack)
paths = ['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif']
plugin = 'aicsimageio-in-memory'
stack = False
_npe2 = <module 'napari.plugins._npe2' from 'C:\Users\Till\mambaforge\envs\vanilla-napari\lib\site-packages\napari\plugins\_npe2.py'>
78 if res is not None:
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\napari\plugins_npe2.py:61, in read(paths=['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'], plugin='aicsimageio-in-memory', stack=False)
60 if 'No readers returned data' not in str(e):
---> 61 raise e from e
62 return None
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\napari\plugins_npe2.py:55, in read(paths=['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'], plugin='aicsimageio-in-memory', stack=False)
54 try:
---> 55 layer_data, reader = io_utils.read_get_reader(
io_utils = <module 'npe2.io_utils' from 'C:\Users\Till\mambaforge\envs\vanilla-napari\lib\site-packages\npe2\io_utils.py'>
npe1_path = 'Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'
plugin = 'aicsimageio-in-memory'
56 npe1_path, plugin_name=plugin
57 )
58 return layer_data, _FakeHookimpl(reader.plugin_name)
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\npe2\io_utils.py:66, in read_get_reader(path='Z:/Till/188_viventis_data/downscaled_mCherry-1.tif', plugin_name='aicsimageio-in-memory', stack=None)
65 new_path, new_stack = v1_to_v2(path)
---> 66 return _read(
new_path = ['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif']
new_stack = False
plugin_name = 'aicsimageio-in-memory'
67 new_path, plugin_name=plugin_name, return_reader=True, stack=new_stack
68 )
69 else:
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\npe2\io_utils.py:169, in _read(paths=['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'], stack=False, plugin_name='aicsimageio-in-memory', return_reader=True, _pm=<npe2._plugin_manager.PluginManager object>)
168 if plugin_name:
--> 169 raise ValueError(
plugin_name = 'aicsimageio-in-memory'
paths = ['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif']
170 f"Plugin {plugin_name!r} was selected to open "
171 + f"{paths!r}, but returned no data."
172 )
173 raise ValueError(f"No readers returned data for {paths!r}")
ValueError: Plugin 'aicsimageio-in-memory' was selected to open ['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'], but returned no data.
The above exception was the direct cause of the following exception:
ValueError Traceback (most recent call last)
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\napari_qt\qt_viewer.py:748, in QtViewer._open_files_dialog(self=<napari._qt.qt_viewer.QtViewer object>, choose_plugin=False)
747 for filename in filenames:
--> 748 self._qt_open(
self = <napari._qt.qt_viewer.QtViewer object at 0x000001CA466F3490>
filename = 'Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'
[filename] = ['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif']
choose_plugin = False
749 [filename], stack=False, choose_plugin=choose_plugin
750 )
751 update_open_history(filenames[0])
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\napari_qt\qt_viewer.py:848, in QtViewer._qt_open(self=<napari._qt.qt_viewer.QtViewer object>, filenames=['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'], stack=False, choose_plugin=False, plugin=None, layer_type=None, **kwargs={})
847 except MultipleReaderError:
--> 848 handle_gui_reading(filenames, self, stack, **kwargs)
filenames = ['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif']
self = <napari._qt.qt_viewer.QtViewer object at 0x000001CA466F3490>
stack = False
kwargs = {}
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\napari_qt\dialogs\qt_reader_dialog.py:199, in handle_gui_reading(paths=['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'], qt_viewer=<napari._qt.qt_viewer.QtViewer object>, stack=False, plugin_name=None, error=None, plugin_override=False, **kwargs={})
198 if display_name:
--> 199 open_with_dialog_choices(
display_name = 'aicsimageio-in-memory'
persist = False
readerDialog = <napari._qt.dialogs.qt_reader_dialog.QtReaderDialog object at 0x000001CA55805900>
readerDialog._extension = '.tif'
readers = {'aicsimageio-in-memory': 'aicsimageio-in-memory', 'aicsimageio-out-of-memory': 'aicsimageio-out-of-memory', 'napari': 'napari builtins'}
paths = ['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif']
stack = False
qt_viewer = <napari._qt.qt_viewer.QtViewer object at 0x000001CA466F3490>
kwargs = {}
200 display_name,
201 persist,
202 readerDialog._extension,
203 readers,
204 paths,
205 stack,
206 qt_viewer,
207 **kwargs,
208 )
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\napari_qt\dialogs\qt_reader_dialog.py:292, in open_with_dialog_choices(display_name='aicsimageio-in-memory', persist=False, extension='.tif', readers={'aicsimageio-in-memory': 'aicsimageio-in-memory', 'aicsimageio-out-of-memory': 'aicsimageio-out-of-memory', 'napari': 'napari builtins'}, paths=['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'], stack=False, qt_viewer=<napari._qt.qt_viewer.QtViewer object>, **kwargs={})
291 # may throw error, but we let it this time
--> 292 qt_viewer.viewer.open(paths, stack=stack, plugin=plugin_name, **kwargs)
plugin_name = 'aicsimageio-in-memory'
paths = ['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif']
qt_viewer.viewer = Viewer(axes=Axes(visible=False, labels=True, colored=True, dashed=False, arrows=True), camera=Camera(center=(0.0, 0.0, 0.0), zoom=1.0, angles=(0.0, 0.0, 90.0), perspective=0.0, interactive=True), cursor=Cursor(position=(1.0, 1.0), scaled=True, size=1, style=<CursorStyle.STANDARD: 'standard'>), dims=Dims(ndim=2, ndisplay=2, last_used=0, range=((0, 2, 1), (0, 2, 1)), current_step=(0, 0), order=(0, 1), axis_labels=('0', '1')), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layers=[], scale_bar=ScaleBar(visible=False, colored=False, color=<class 'numpy.ndarray'> (4,) float32, ticks=True, position=<Position.BOTTOM_RIGHT: 'bottom_right'>, font_size=10.0, box=False, box_color=<class 'numpy.ndarray'> (4,) float32, unit=None), text_overlay=TextOverlay(visible=False, color=<class 'numpy.ndarray'> (4,) float32, font_size=10.0, position=<TextOverlayPosition.TOP_LEFT: 'top_left'>, text=''), overlays=Overlays(interaction_box=InteractionBox(points=None, show=False, show_handle=False, show_vertices=False, selection_box_drag=None, selection_box_final=None, transform_start=<napari.utils.transforms.transforms.Affine object at 0x000001CA3FAA4EE0>, transform_drag=<napari.utils.transforms.transforms.Affine object at 0x000001CA3FAA4F40>, transform_final=<napari.utils.transforms.transforms.Affine object at 0x000001CA3FAA4FA0>, transform=<napari.utils.transforms.transforms.Affine object at 0x000001CA3FAA5000>, allow_new_selection=True, selected_vertex=None)), help='', status='Ready', tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_over_canvas=True, mouse_move_callbacks=[<function InteractionBoxMouseBindings.initialize_mouse_events..mouse_move at 0x000001CA51722680>], mouse_drag_callbacks=[<function InteractionBoxMouseBindings.initialize_mouse_events..mouse_drag at 0x000001CA51722950>], mouse_double_click_callbacks=[], mouse_wheel_callbacks=[<function dims_scroll at 0x000001CA4560EEF0>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keymap={'Shift': <function InteractionBoxMouseBindings.initialize_key_events..hold_to_lock_aspect_ratio at 0x000001CA517227A0>, 'Control-Shift-R': <function InteractionBoxMouseBindings._reset_active_layer_affine at 0x000001CA520F40D0>, 'Control-Shift-A': <function InteractionBoxMouseBindings._transform_active_layer at 0x000001CA520F4C10>})
stack = False
kwargs = {}
qt_viewer = <napari._qt.qt_viewer.QtViewer object at 0x000001CA466F3490>
294 if persist:
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\napari\components\viewer_model.py:1014, in ViewerModel.open(self=Viewer(axes=Axes(visible=False, labels=True, col...._transform_active_layer at 0x000001CA520F4C10>}), path=['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'], stack=False, plugin='aicsimageio-in-memory', layer_type=None, **kwargs={})
1012 if plugin:
1013 added.extend(
-> 1014 self._add_layers_with_plugins(
added = []
self = Viewer(axes=Axes(visible=False, labels=True, colored=True, dashed=False, arrows=True), camera=Camera(center=(0.0, 0.0, 0.0), zoom=1.0, angles=(0.0, 0.0, 90.0), perspective=0.0, interactive=True), cursor=Cursor(position=(1.0, 1.0), scaled=True, size=1, style=<CursorStyle.STANDARD: 'standard'>), dims=Dims(ndim=2, ndisplay=2, last_used=0, range=((0, 2, 1), (0, 2, 1)), current_step=(0, 0), order=(0, 1), axis_labels=('0', '1')), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layers=[], scale_bar=ScaleBar(visible=False, colored=False, color=<class 'numpy.ndarray'> (4,) float32, ticks=True, position=<Position.BOTTOM_RIGHT: 'bottom_right'>, font_size=10.0, box=False, box_color=<class 'numpy.ndarray'> (4,) float32, unit=None), text_overlay=TextOverlay(visible=False, color=<class 'numpy.ndarray'> (4,) float32, font_size=10.0, position=<TextOverlayPosition.TOP_LEFT: 'top_left'>, text=''), overlays=Overlays(interaction_box=InteractionBox(points=None, show=False, show_handle=False, show_vertices=False, selection_box_drag=None, selection_box_final=None, transform_start=<napari.utils.transforms.transforms.Affine object at 0x000001CA3FAA4EE0>, transform_drag=<napari.utils.transforms.transforms.Affine object at 0x000001CA3FAA4F40>, transform_final=<napari.utils.transforms.transforms.Affine object at 0x000001CA3FAA4FA0>, transform=<napari.utils.transforms.transforms.Affine object at 0x000001CA3FAA5000>, allow_new_selection=True, selected_vertex=None)), help='', status='Ready', tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_over_canvas=True, mouse_move_callbacks=[<function InteractionBoxMouseBindings.initialize_mouse_events..mouse_move at 0x000001CA51722680>], mouse_drag_callbacks=[<function InteractionBoxMouseBindings.initialize_mouse_events..mouse_drag at 0x000001CA51722950>], mouse_double_click_callbacks=[], mouse_wheel_callbacks=[<function dims_scroll at 0x000001CA4560EEF0>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keymap={'Shift': <function InteractionBoxMouseBindings.initialize_key_events..hold_to_lock_aspect_ratio at 0x000001CA517227A0>, 'Control-Shift-R': <function InteractionBoxMouseBindings._reset_active_layer_affine at 0x000001CA520F40D0>, 'Control-Shift-A': <function InteractionBoxMouseBindings._transform_active_layer at 0x000001CA520F4C10>})
_path = ['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif']
kwargs = {}
plugin = 'aicsimageio-in-memory'
layer_type = None
_stack = False
1015 _path,
1016 kwargs=kwargs,
1017 plugin=plugin,
1018 layer_type=layer_type,
1019 stack=_stack,
1020 )
1021 )
1022 # no plugin choice was made
1023 else:
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\napari\components\viewer_model.py:1216, in ViewerModel._add_layers_with_plugins(self=Viewer(axes=Axes(visible=False, labels=True, col...._transform_active_layer at 0x000001CA520F4C10>}), paths=['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'], stack=False, kwargs={}, plugin='aicsimageio-in-memory', layer_type=None)
1215 assert len(paths) == 1
-> 1216 layer_data, hookimpl = read_data_with_plugins(
paths = ['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif']
stack = False
plugin = 'aicsimageio-in-memory'
1217 paths, plugin=plugin, stack=stack
1218 )
1220 # glean layer names from filename. These will be used as fallback
1221 # names, if the plugin does not return a name kwarg in their meta dict.
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\napari\plugins\io.py:77, in read_data_with_plugins(paths=['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'], plugin='aicsimageio-in-memory', stack=False)
75 hookimpl: Optional[HookImplementation]
---> 77 res = _npe2.read(paths, plugin, stack=stack)
paths = ['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif']
plugin = 'aicsimageio-in-memory'
stack = False
_npe2 = <module 'napari.plugins._npe2' from 'C:\Users\Till\mambaforge\envs\vanilla-napari\lib\site-packages\napari\plugins\_npe2.py'>
78 if res is not None:
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\napari\plugins_npe2.py:61, in read(paths=['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'], plugin='aicsimageio-in-memory', stack=False)
60 if 'No readers returned data' not in str(e):
---> 61 raise e from e
62 return None
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\napari\plugins_npe2.py:55, in read(paths=['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'], plugin='aicsimageio-in-memory', stack=False)
54 try:
---> 55 layer_data, reader = io_utils.read_get_reader(
io_utils = <module 'npe2.io_utils' from 'C:\Users\Till\mambaforge\envs\vanilla-napari\lib\site-packages\npe2\io_utils.py'>
npe1_path = 'Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'
plugin = 'aicsimageio-in-memory'
56 npe1_path, plugin_name=plugin
57 )
58 return layer_data, _FakeHookimpl(reader.plugin_name)
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\npe2\io_utils.py:66, in read_get_reader(path='Z:/Till/188_viventis_data/downscaled_mCherry-1.tif', plugin_name='aicsimageio-in-memory', stack=None)
65 new_path, new_stack = v1_to_v2(path)
---> 66 return _read(
new_path = ['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif']
new_stack = False
plugin_name = 'aicsimageio-in-memory'
67 new_path, plugin_name=plugin_name, return_reader=True, stack=new_stack
68 )
69 else:
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\npe2\io_utils.py:169, in _read(paths=['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'], stack=False, plugin_name='aicsimageio-in-memory', return_reader=True, _pm=<npe2._plugin_manager.PluginManager object>)
168 if plugin_name:
--> 169 raise ValueError(
plugin_name = 'aicsimageio-in-memory'
paths = ['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif']
170 f"Plugin {plugin_name!r} was selected to open "
171 + f"{paths!r}, but returned no data."
172 )
173 raise ValueError(f"No readers returned data for {paths!r}")
ValueError: Plugin 'aicsimageio-in-memory' was selected to open ['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'], but returned no data.
The above exception was the direct cause of the following exception:
ValueError Traceback (most recent call last)
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\napari_qt\qt_viewer.py:748, in QtViewer._open_files_dialog(self=<napari._qt.qt_viewer.QtViewer object>, choose_plugin=False)
746 if (filenames != []) and (filenames is not None):
747 for filename in filenames:
--> 748 self._qt_open(
self = <napari._qt.qt_viewer.QtViewer object at 0x000001CA466F3490>
filename = 'Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'
[filename] = ['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif']
choose_plugin = False
749 [filename], stack=False, choose_plugin=choose_plugin
750 )
751 update_open_history(filenames[0])
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\napari_qt\qt_viewer.py:848, in QtViewer._qt_open(self=<napari._qt.qt_viewer.QtViewer object>, filenames=['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'], stack=False, choose_plugin=False, plugin=None, layer_type=None, **kwargs={})
838 handle_gui_reading(
839 filenames,
840 self,
(...)
845 **kwargs,
846 )
847 except MultipleReaderError:
--> 848 handle_gui_reading(filenames, self, stack, **kwargs)
filenames = ['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif']
self = <napari._qt.qt_viewer.QtViewer object at 0x000001CA466F3490>
stack = False
kwargs = {}
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\napari_qt\dialogs\qt_reader_dialog.py:199, in handle_gui_reading(paths=['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'], qt_viewer=<napari._qt.qt_viewer.QtViewer object>, stack=False, plugin_name=None, error=None, plugin_override=False, **kwargs={})
197 display_name, persist = readerDialog.get_user_choices()
198 if display_name:
--> 199 open_with_dialog_choices(
display_name = 'aicsimageio-in-memory'
persist = False
readerDialog = <napari._qt.dialogs.qt_reader_dialog.QtReaderDialog object at 0x000001CA55805900>
readerDialog._extension = '.tif'
readers = {'aicsimageio-in-memory': 'aicsimageio-in-memory', 'aicsimageio-out-of-memory': 'aicsimageio-out-of-memory', 'napari': 'napari builtins'}
paths = ['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif']
stack = False
qt_viewer = <napari._qt.qt_viewer.QtViewer object at 0x000001CA466F3490>
kwargs = {}
200 display_name,
201 persist,
202 readerDialog._extension,
203 readers,
204 paths,
205 stack,
206 qt_viewer,
207 **kwargs,
208 )
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\napari_qt\dialogs\qt_reader_dialog.py:292, in open_with_dialog_choices(display_name='aicsimageio-in-memory', persist=False, extension='.tif', readers={'aicsimageio-in-memory': 'aicsimageio-in-memory', 'aicsimageio-out-of-memory': 'aicsimageio-out-of-memory', 'napari': 'napari builtins'}, paths=['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'], stack=False, qt_viewer=<napari._qt.qt_viewer.QtViewer object>, **kwargs={})
288 plugin_name = [
289 p_name for p_name, d_name in readers.items() if d_name == display_name
290 ][0]
291 # may throw error, but we let it this time
--> 292 qt_viewer.viewer.open(paths, stack=stack, plugin=plugin_name, **kwargs)
plugin_name = 'aicsimageio-in-memory'
paths = ['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif']
qt_viewer.viewer = Viewer(axes=Axes(visible=False, labels=True, colored=True, dashed=False, arrows=True), camera=Camera(center=(0.0, 0.0, 0.0), zoom=1.0, angles=(0.0, 0.0, 90.0), perspective=0.0, interactive=True), cursor=Cursor(position=(1.0, 1.0), scaled=True, size=1, style=<CursorStyle.STANDARD: 'standard'>), dims=Dims(ndim=2, ndisplay=2, last_used=0, range=((0, 2, 1), (0, 2, 1)), current_step=(0, 0), order=(0, 1), axis_labels=('0', '1')), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layers=[], scale_bar=ScaleBar(visible=False, colored=False, color=<class 'numpy.ndarray'> (4,) float32, ticks=True, position=<Position.BOTTOM_RIGHT: 'bottom_right'>, font_size=10.0, box=False, box_color=<class 'numpy.ndarray'> (4,) float32, unit=None), text_overlay=TextOverlay(visible=False, color=<class 'numpy.ndarray'> (4,) float32, font_size=10.0, position=<TextOverlayPosition.TOP_LEFT: 'top_left'>, text=''), overlays=Overlays(interaction_box=InteractionBox(points=None, show=False, show_handle=False, show_vertices=False, selection_box_drag=None, selection_box_final=None, transform_start=<napari.utils.transforms.transforms.Affine object at 0x000001CA3FAA4EE0>, transform_drag=<napari.utils.transforms.transforms.Affine object at 0x000001CA3FAA4F40>, transform_final=<napari.utils.transforms.transforms.Affine object at 0x000001CA3FAA4FA0>, transform=<napari.utils.transforms.transforms.Affine object at 0x000001CA3FAA5000>, allow_new_selection=True, selected_vertex=None)), help='', status='Ready', tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_over_canvas=True, mouse_move_callbacks=[<function InteractionBoxMouseBindings.initialize_mouse_events..mouse_move at 0x000001CA51722680>], mouse_drag_callbacks=[<function InteractionBoxMouseBindings.initialize_mouse_events..mouse_drag at 0x000001CA51722950>], mouse_double_click_callbacks=[], mouse_wheel_callbacks=[<function dims_scroll at 0x000001CA4560EEF0>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keymap={'Shift': <function InteractionBoxMouseBindings.initialize_key_events..hold_to_lock_aspect_ratio at 0x000001CA517227A0>, 'Control-Shift-R': <function InteractionBoxMouseBindings._reset_active_layer_affine at 0x000001CA520F40D0>, 'Control-Shift-A': <function InteractionBoxMouseBindings._transform_active_layer at 0x000001CA520F4C10>})
stack = False
kwargs = {}
qt_viewer = <napari._qt.qt_viewer.QtViewer object at 0x000001CA466F3490>
294 if persist:
295 if not extension.endswith(os.sep):
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\napari\components\viewer_model.py:1014, in ViewerModel.open(self=Viewer(axes=Axes(visible=False, labels=True, col...._transform_active_layer at 0x000001CA520F4C10>}), path=['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'], stack=False, plugin='aicsimageio-in-memory', layer_type=None, **kwargs={})
1011 _path = [_path] if not isinstance(_path, list) else _path
1012 if plugin:
1013 added.extend(
-> 1014 self._add_layers_with_plugins(
added = []
self = Viewer(axes=Axes(visible=False, labels=True, colored=True, dashed=False, arrows=True), camera=Camera(center=(0.0, 0.0, 0.0), zoom=1.0, angles=(0.0, 0.0, 90.0), perspective=0.0, interactive=True), cursor=Cursor(position=(1.0, 1.0), scaled=True, size=1, style=<CursorStyle.STANDARD: 'standard'>), dims=Dims(ndim=2, ndisplay=2, last_used=0, range=((0, 2, 1), (0, 2, 1)), current_step=(0, 0), order=(0, 1), axis_labels=('0', '1')), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layers=[], scale_bar=ScaleBar(visible=False, colored=False, color=<class 'numpy.ndarray'> (4,) float32, ticks=True, position=<Position.BOTTOM_RIGHT: 'bottom_right'>, font_size=10.0, box=False, box_color=<class 'numpy.ndarray'> (4,) float32, unit=None), text_overlay=TextOverlay(visible=False, color=<class 'numpy.ndarray'> (4,) float32, font_size=10.0, position=<TextOverlayPosition.TOP_LEFT: 'top_left'>, text=''), overlays=Overlays(interaction_box=InteractionBox(points=None, show=False, show_handle=False, show_vertices=False, selection_box_drag=None, selection_box_final=None, transform_start=<napari.utils.transforms.transforms.Affine object at 0x000001CA3FAA4EE0>, transform_drag=<napari.utils.transforms.transforms.Affine object at 0x000001CA3FAA4F40>, transform_final=<napari.utils.transforms.transforms.Affine object at 0x000001CA3FAA4FA0>, transform=<napari.utils.transforms.transforms.Affine object at 0x000001CA3FAA5000>, allow_new_selection=True, selected_vertex=None)), help='', status='Ready', tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_over_canvas=True, mouse_move_callbacks=[<function InteractionBoxMouseBindings.initialize_mouse_events..mouse_move at 0x000001CA51722680>], mouse_drag_callbacks=[<function InteractionBoxMouseBindings.initialize_mouse_events..mouse_drag at 0x000001CA51722950>], mouse_double_click_callbacks=[], mouse_wheel_callbacks=[<function dims_scroll at 0x000001CA4560EEF0>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keymap={'Shift': <function InteractionBoxMouseBindings.initialize_key_events..hold_to_lock_aspect_ratio at 0x000001CA517227A0>, 'Control-Shift-R': <function InteractionBoxMouseBindings._reset_active_layer_affine at 0x000001CA520F40D0>, 'Control-Shift-A': <function InteractionBoxMouseBindings._transform_active_layer at 0x000001CA520F4C10>})
_path = ['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif']
kwargs = {}
plugin = 'aicsimageio-in-memory'
layer_type = None
_stack = False
1015 _path,
1016 kwargs=kwargs,
1017 plugin=plugin,
1018 layer_type=layer_type,
1019 stack=_stack,
1020 )
1021 )
1022 # no plugin choice was made
1023 else:
1024 layers = self._open_or_raise_error(
1025 _path, kwargs, layer_type, _stack
1026 )
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\napari\components\viewer_model.py:1216, in ViewerModel._add_layers_with_plugins(self=Viewer(axes=Axes(visible=False, labels=True, col...._transform_active_layer at 0x000001CA520F4C10>}), paths=['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'], stack=False, kwargs={}, plugin='aicsimageio-in-memory', layer_type=None)
1214 else:
1215 assert len(paths) == 1
-> 1216 layer_data, hookimpl = read_data_with_plugins(
paths = ['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif']
stack = False
plugin = 'aicsimageio-in-memory'
1217 paths, plugin=plugin, stack=stack
1218 )
1220 # glean layer names from filename. These will be used as fallback
1221 # names, if the plugin does not return a name kwarg in their meta dict.
1222 filenames = []
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\napari\plugins\io.py:77, in read_data_with_plugins(paths=['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'], plugin='aicsimageio-in-memory', stack=False)
74 assert len(paths) == 1
75 hookimpl: Optional[HookImplementation]
---> 77 res = _npe2.read(paths, plugin, stack=stack)
paths = ['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif']
plugin = 'aicsimageio-in-memory'
stack = False
_npe2 = <module 'napari.plugins._npe2' from 'C:\Users\Till\mambaforge\envs\vanilla-napari\lib\site-packages\napari\plugins\_npe2.py'>
78 if res is not None:
79 _ld, hookimpl = res
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\napari\plugins_npe2.py:61, in read(paths=['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'], plugin='aicsimageio-in-memory', stack=False)
59 except ValueError as e:
60 if 'No readers returned data' not in str(e):
---> 61 raise e from e
62 return None
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\napari\plugins_npe2.py:55, in read(paths=['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'], plugin='aicsimageio-in-memory', stack=False)
53 npe1_path = paths[0]
54 try:
---> 55 layer_data, reader = io_utils.read_get_reader(
io_utils = <module 'npe2.io_utils' from 'C:\Users\Till\mambaforge\envs\vanilla-napari\lib\site-packages\npe2\io_utils.py'>
npe1_path = 'Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'
plugin = 'aicsimageio-in-memory'
56 npe1_path, plugin_name=plugin
57 )
58 return layer_data, _FakeHookimpl(reader.plugin_name)
59 except ValueError as e:
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\npe2\io_utils.py:66, in read_get_reader(path='Z:/Till/188_viventis_data/downscaled_mCherry-1.tif', plugin_name='aicsimageio-in-memory', stack=None)
62 if stack is None:
63 # "npe1" old path
64 # Napari 0.4.15 and older, hopefully we can drop this and make stack mandatory
65 new_path, new_stack = v1_to_v2(path)
---> 66 return _read(
new_path = ['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif']
new_stack = False
plugin_name = 'aicsimageio-in-memory'
67 new_path, plugin_name=plugin_name, return_reader=True, stack=new_stack
68 )
69 else:
70 assert isinstance(path, list)
File ~\mambaforge\envs\vanilla-napari\lib\site-packages\npe2\io_utils.py:169, in _read(paths=['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'], stack=False, plugin_name='aicsimageio-in-memory', return_reader=True, _pm=<npe2._plugin_manager.PluginManager object>)
166 return (layer_data, rdr) if return_reader else layer_data
168 if plugin_name:
--> 169 raise ValueError(
plugin_name = 'aicsimageio-in-memory'
paths = ['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif']
170 f"Plugin {plugin_name!r} was selected to open "
171 + f"{paths!r}, but returned no data."
172 )
173 raise ValueError(f"No readers returned data for {paths!r}")
ValueError: Plugin 'aicsimageio-in-memory' was selected to open ['Z:/Till/188_viventis_data/downscaled_mCherry-1.tif'], but returned no data.
steps to reproduce (on Windows 11 with mambaforge):
in napari go to file->open and select a tif file and choose aicsimageio as reader plugin (example.zip contains file that I used for testing)
mamba list output
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